SWISS-MODEL Repository 
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SWISS-MODEL Repository - Model Details
Model Overview
Sequence
Domain
Model 3D Structure
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Template Links:
[ RCSB ]
[ PDBe ]
[ SCOP ]
[ CATH ]
display model: in [ AstexViewer ] download model: as [ pdb ] - as [ Deepview project ] 
This model has not been updated since 2013-01-30. In the meantime, new template
structures may have become available which would allow building a more reliable model.
Would you like to submit the target protein to SWISS-MODEL Workspace and build a new model now?
[ Submit ]
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Alignment
TARGET 1 V TEYTYDNLRK
1v25B 8 afpstmmdee lnlwdflera aalfgrkevv srlhtge--v hrttyaevyq
TARGET hhhhhh
1v25B hhhhhhh hhh ssss sss s s ssssshhhhh
TARGET 12 DVYRIATSLR NYGIGPGDTV CGFVPNTYDT LVAVFATAAV GAAWCSASVD
1v25B 56 rarrlmgglr algvgvgdrv atlgfnhfrh leayfavpgm gavlhtanpr
TARGET hhhhhhhhhh hh sss sss hhh hhhhhhhhh sssss
1v25B hhhhhhhhhh hh sss sss hhh hhhhhhhhh sssss
TARGET 62 FGPAGVLDRF RQVHPKVLFT VNHVTYKKKL ID--QTDKIN EIVKELPTLE
1v25B 106 lspk------ -----eiayi lnhaedkvll fdpnllplve airgelktvq
TARGET hhhh hhhh sss ss hhhh hh
1v25B hh hhhhh hhhh sss ss hhhhh h
TARGET 110 KIVVSDTFTS VKFDATKYNQ SDKFSSLEEF KTPIADVVLP FVYTPVPFSD
1v25B 145 hfvvmde--- --------ka pegylayeea lgeeadpv-- ----rvpera
TARGET ssssssssss sssss ssshhh
1v25B sssss ssshhh
TARGET 160 PLFVMFSSGT TGIPKAMVHT VGGTLLKHIE EHLVQGDS - ----------
1v25B 178 acgmayttgt tglpkgvvys hralvlhsla aslvdgtals ekdvvlpvvp
TARGET ssssss sssss hhhhhhhhhh h
1v25B ssssss sssss hhhhhhhhhh h ssssss
TARGET ---------- ---------- ---------- ---------- ----------
1v25B 228 mfhvnawclp yaatlvgakq vlpgprldpa slvelfdgeg vtftagvptv
TARGET
1v25B hh hhhhhh ss ss hh hhhhhhhh sssss hh
TARGET ---------- ---------- ---------- ---------- ----------
1v25B 278 wlaladyles tghrlktlrr lvvggsaapr sliarfermg vevrqgyglt
TARGET
1v25B hhhhhhhhhh h ss ssss h hhhhhhhh ssssss
TARGET ---------- ---------- ---------- ---------- ----------
1v25B 328 etspvvvqnf vkshleslse eekltlkakt glpiplvrlr vadeegrpvp
TARGET
1v25B ssss h hhhhhhh sss sss sss sss
TARGET ---------- ---------- ---------- ---------- ----------
1v25B 378 kdgkalgevq lkgpwitggy ygneeatrsa ltpdgffrtg diavwdeegy
TARGET
1v25B sss ssss ss hhhhhh ssss sssssss s
TARGET ---------- ---------- ---------- ---------- ----------
1v25B 428 veikdrlkdl iksggewiss vdlenalmgh aavvaiphpk wqerplavne
TARGET
1v25B sssssss sss sss h hhhhhhhh sssss sssss h
TARGET ---------- ---------- ---------- -------
1v25B 496 hllkagfakw qlpdayvfgk flkralreqy knyygga
TARGET
1v25B hhhh hhhhhh
Template's ligands section
Ligands in the template:ANP : 1,MG : 1.
Ligands in the template that will be assessed: ANP1666, MG1002.
Model's ligands section
ANP1666
ANP1666 interacts, within a radius of 3 Angstroem, with the following ions: MG1002. They will be considered as a single ligand.
Not all the residues interacting with the ligand are completely conserved between model and template.
No RMSD calculation will be performed.
Given the properties calculated previously, the ligand ANP1666 will not be included in the model.
ANP1666: conservation:False, RMSD:False, included: False
No ligands were included in the model.
Quaternary Structure Annotation of the Template
1v25 is annotated as DIMER
The oligomeric state of the structure was assigned by the authors of the corresponding PDB entry
The following biological unit was used to build the template structure: 1v25.pdb1.gz
Quaternary Structure Modelling of the Target Protein
Analysis of evolutionary and family specific aspects revealed non-conservation of the oligomeric structure
Hence, the oligomeric structures of the target and the template cannot be assumed to be similar (=DIMER)
The target structure was calculated as SINGLE CHAIN
The corresponding reliability score is 0.028 (>0.5 indicates similarity)
To build the complex the following chains of the complex has been additionally identified: 1v25A
Template Selection
- Start SMR-Pipeline for:d6e7612cd22923c663d5ad4e096b3b9c on BC2-cluster at Thu Feb 21 08:43:58
2013
- Analyze BLAST summary ...
- No templates found with BLAST (seqid-cutoff: 60): go to HHSEARCH
- Run HHSearch to detect more templates...
- Generate new template library
- Run template selection against modfied template library
- Summarize templates:
- Proof template(s) selection compared to previous Repository update
- Different number of templates selected (old0 vs new:3): model based on new templates
- Send 3 Templates for modeling
- @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
- ***********************
- building model based on 1v25B (154-350) was successful
- ****************************************************************
- building model based on 1ry2A (122-680) was successful
- *********************************************************
- building model based on 4gr5C (72-570) was not successful go to next best template
- *********************************************************
- building model based on 4gr4C (73-571) was not successful go to next best template
- Repository Pipeline parameter
Cut-off parameters to model the target based on a BLAST target-template alignment
Evalue : 0.0001
Minimum Template size (aa) for ranking : 25
Minimum Sequence identity : 60
Cut-off parameters to model the target based on a HHSearch target-template alignment
Evalue : 0.0001
Probability : 50
MAC : 0.3
Parameters for model selection
Minimal number of uncovered target
residues after BLAST to run HHSEARCH : 50
Minimal number of uncovered target
residues to model an additional template : 25
- Finish SMR-Pipeline for:d6e7612cd22923c663d5ad4e096b3b9c on BC2-cluster at Thu Feb 21 08:51:53
2013
Template Search
| Template Description |
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4gr5: CRYSTAL STRUCTURE OF SLGN1DELTAASUB IN COMPLEX WITH AMPCPP Solved by: X-RAY, Resolution: 1.92A, Identified by HHSEARCH |
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4gr4: CRYSTAL STRUCTURE OF SLGN1DELTAASUB Solved by: X-RAY, Resolution: 2.44A, Identified by HHSEARCH |
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3ipl: CRYSTAL STRUCTURE OF O-SUCCINYLBENZOIC ACID-COA LIGASE FROSTAPHYLOCOCCUS AUREUS SUBSP. AUREUS MU50 Solved by: X-RAY, Resolution: 2.30A, Identified by HHSEARCH |
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4b2g: CRYSTAL STRUCTURE OF AN INDOLE-3-ACETIC ACID AMIDO SYNTHASFROM VITIS VINIFERA INVOLVED IN AUXIN HOMEOSTASIS Solved by: X-RAY, Resolution: 2.40A, Identified by HHSEARCH |
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Downloads
Reference
If you are using models from the SWISS-MODEL Repository, please cite the following articles:
- Kiefer F, Arnold K, Künzli M, Bordoli L, Schwede T (2009).
The SWISS-MODEL Repository and associated resources.
Nucleic Acids Res. 37, D387-D392.
- Jürgen Kopp and Torsten Schwede (2004)
The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models.
Nucleic Acids Res. 32, D230-D234.